Frame of Mind
by Phoenix Nova
Summary: Sheppard is still haunted by the Iratus Bug. But when strange things begin happening on Atlantis, Sheppard begins to question who he can still trust.
1. CH 1: Unlikely Alliance

This is a really interesting story idea I had, I have never written some of these characters, so it will be interesting to see where things go. But I promise a twisted twist in the end.

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Stargate Atlantis: Frame of Mind

**CH 1 - Unlikely Alliance**

Lt. Ford looked down at Colonel Sheppard, and the huge bug that had attached itself to the colonel.

The tendrils wiggled as they held onto Sheppard.

Sheppard abruptly woke from the dream, and he went to the mirror.

Turning on the light Sheppard was able o glance into the mirror and look at where the stinger had penetrated his neck nearly three years earlier. He could still feel where the stinger went in, and the tendrils on the Iratus Bug, still wrapped around his neck.

Sheppard splashed a bit of cold water onto his face, and rubbed the water around until it looked like large beads of sweat.

Reaching for a towel he heard the door chime.

"Come in." Sheppard called.

The door didn't open.

a full minute later the door chime sounded again.

"Come in." Sheppard called again.

Again, the door didn't open.

"Someone has a twisted idea of a joke." Sheppard commented gritting his teeth.

The door chimed a third time, after another minute.

"Come in!" Sheppard shouted.

Major Lorne came in "Sir?"

"Major Lorne?" Sheppard asked.

"Is everything alright, sir?" Major Lorne asked.

"Didn't you hear me the first time Major?" Sheppard demanded.

"I only used the door chime one time, sir." Lorne defended.

"Once." Sheppard confirmed, then was lost in thought for a second. "Did you see anyone in the halls before you got here?" Sheppard asked, thinking someone had a sick idea of a practical joke.

"No one, sir." Lorne replied, then reversed to his original question. "Is everything alright, sir?" Major Lorne asked.

"I don't sleep well any more, I keep having a dream about the Iratus bug." Sheppard replied rubbing his face.

"Maybe you should go to the infirmary." Major Lorne suggested.

"Couldn't hurt." Sheppard agreed, then wondered why Major Lorne was there. "Why are you here?"

"You weren't responding on the radio. Dr. Weir needs you in Stargate Ops." Major Lorne replied.

"I'll go to the infirmary after I see what Elizabeth wants." Sheppard decided.

Major Lorne walked with Sheppard back to the control tower.

Seeing the expeditions leader Sheppard greeted her.

"You wanted to see me, Elizabeth?"

"Yes, John. We receive a message from the M9X-442. It appears there is a Wraith hive ship on the way."

"And you want me to . . ." Sheppard stopped, he had seen something he did not expect . . . a Wraith sitting in Weir's office. No restraints, no guards. He was a threat, Sheppard was the only one that cared.

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I hope this turned out ok, I know that the first chapter is short, and I hope that it has the impact for you that I think it has. Any way, read, review, enjoy.


	2. CH 2: The Poison called Suspicion

Thanks for your reads, reviews, and input, I hope you all enjoy this chapter, I think it tuned out okay. Read for yourself.

Stargate Atlantis: Frame of Mind

**Chapter 2: The Poison called Suspicion.**

Sheppard grabbed the side arm from a nearby marine, and pointed towards Dr. Weir's office.

"John, what are you doing?" Elizabeth demanded.

Sheppard looked into Weir's office, the Wraith was gone.

"John?" Weir asked.

"Sorry, I thought I saw." Sheppard paused, questioning if what he just saw was real.

"Saw what, John?" Weir asked.

"Nothing." Sheppard finally said.

"Go see, Dr. Beckett." Weir ordered. Then sense Sheppard might resist. "That wasn't a request."

"I'll just go to the infirmary." Sheppard said. Then relinquished the weapon and turned to walk out of the room.

Somehow the corridor seemed dark, almost sinister. Dread seemed to hang in the air.

A leering feeling fell over Colonel Sheppard. The feeling that someone was watching him. As he continued down the corridor the feeling got stronger.

Stopping he listened, thinking he heard something.

When he heard nothing he continued.

After ten meters he stopped again, he definitely heard something.

The sound of breathing. Breathing he only heard one other time. While in Kolya's custody, when he met a fellow captive. The sound of a starving Wraith.

Sheppard broke into a dead run, determined to make it to a nearby transporter.

The sound of the starving Wraith grew louder, the closer Sheppard got to the transporter. Until finally Sheppard arrived at the transporter only to have the door open to reveal a Wraith.

The Wraith was obviously starving and looking downward, but his eyes moved up to meet Sheppard's gaze. Then he lunged at Sheppard and began to feed on him causing Sheppard to bolt up from an examination table.

"Where am I?" Sheppard asked dazed and confused.

"The infirmary, I _WAS_ running a scan on you just a moment ago." The Scottish doctor replied with a patient tone, laced with trace amounts of irritation.

Sheppard looked up and noticed the scanner moving back towards him.

"Just relax, the scan will be done in a moment." Carson urged.

Sheppard laid back down, and conceded to the fact he might have been dreaming.

Moments later the scan was complete and Carson returned to discuss the results, or lack there of.

"As far as I can tell you're as healthy as a horse. Your scan was pristine. I found nothing out of the ordinary."

Beckett handed Sheppard some medication.

"These will help you sleep, all you need is eight hours of uninterrupted sleep." Beckett assured, and dismissed Sheppard.

Sheppard had a funny feeling, not 'ha-ha' funny, but sinister, so when he left the infirmary he paused just outside the door, but out of sight. Soon Carson was on his radio, what Sheppard overheard made him wonder what else was going on.

"Dr. Weir, this is Dr. Beckett."

"Yes, he left a few moments ago."

"No he didn't seem to suspect anything. Is the Wraith still in your office?"

"Aye, will do, Beckett out."

I hope you enjoyed the chapter, twist and all. Chapter 3 will be coming shortly.


	3. CH 3: Metamorphosis

This is an idea I had, I have the feeling that I'll have to write something to make up for this chapter, I feel it didn't turn out too well, but it was interesting.

Stargate Atlantis: Frame of Mind

**Chapter 3 - Metamorphosis**

Sheppard looked at the pills that Carson gave him, and suddenly had an overwhelming curiosity. Not knowing who he could trust, he decided to take a chance on Rodney McKay.

Sheppard found McKay in the mess with a fresh cup of coffee.

"Rodney, to talk to you." Sheppard asked.

"I didn't do it." Rodney said, jumping to a conclusion.

Sheppard glanced around at the various people in the mess, not knowing if anyone else had been compromised, then spoke in a low tone.

"Weir has a Wraith in her office, there's no guard, and no precautions." Sheppard began.

"Really?" Rodney said, fear replacing his hunger.

"Something is going on here." Sheppard said.

"You just can't prove it." Rodney concluded.

"Beckett gave me these. But I think they might not be what he says they are." Sheppard said producing the pills Beckett gave him half an hour earlier.

"What make you so sure they're tainted?" Rodney asked.

"I overheard Beckett talking to Elizabeth over the radio." Sheppard replied.

"We can check them out in my lab." Rodney quietly said.

Sheppard nodded in agreement, and Rodney lead the way.

As they walked to Rodney's lab, Sheppard felt like everybody's eyes were on him.

Rodney noticed. "Are you okay?"

"Yeah." Sheppard replied "Probably just paranoia."

Arriving at McKay's lab Rodney went for his laptop, intent on hacking into the medical database.

Sheppard caught a quick glance up and spotted a Wraith, but not any Wraith, this one was familiar. He just stood there and watched intently.

Sheppard lost track of Rodney. Finally McKay started snapping his fingers multiple times in quick succession, trying to get Sheppard's attention.

"Sorry." Then Sheppard pointed to where he saw Todd, bt he was gone.

"Yes, that's the door. Hopefully no one will come through it." McKay said mockingly.

Soon McKay was in.

After two minutes they found something of interest.

"Well this is interesting." Rodney began, reading to himself.

"What?" Sheppard asked.

"Well, turns out those pills Carson gave you contain the Wraith retro virus." Rodney explained.

"The Retro Virus?" Sheppard repeated. "Why would Beckett give me his retro virus?" Sheppard wondered.

"I'm not sure. But according to this, Carson, Weir, and about two dozen others have been taking these." Rodney said.

Something was off about Rodney's reply. But that didn't matter, something began happening, Sheppard was having vague recollections of some disturbing events. Feeding on a human.

Rodney noticed, and went for his radio to call for help.

"Beckett this is McKay, I need some help in my lab."

More quickly than normal, Sheppard went pale, his voice changed, and his hair turned white as snow. Then Sheppard thrust his hand against Rodney's chest. He was feeding on Rodney.

As the husky that was once Rodney McKay dropped to the ground, the door opened.

It was Todd.

"You're not one of us, John Sheppard."

Sheppard woke up to a clap of thunder outside the window of his quarters, and the tapping sound of rain on the window.

Feel free to leave constructive criticism, whether it's mean or nice I can only learn from it. Thanks, God bless.


	4. CH 4: Paranoia or Conspiracy?

I recognize that some of my readers maybe confused, that's kind of what I was going for, the whole ST:TNG episode with the same title.

And yes, in the dream at the end of Ch 3 Sheppard was transforming into a Wraith.

Stargate Atlantis: Frame of Mind

Ch 4 - Paranoia or Conspiracy?

Sheppard sat on the edge of his bed, rubbing his, trying to forget about the horrible dream he just woke from. He could still see Rodney's body lying on the ground, a husk that fell victim to a Wraith's insatiable hunger.

The door chimed.

"Come in." Sheppard said, standing from his bed.

The door didn't open.

Sheppard went to the door and waved his hand across the blue crystal sensor, the door opened, and Sheppard stepped out.

A pale hand wrapped itself around Sheppards neck. Sheppard saw the hand and his eyes followed it to an arm, and then to the pale, wild eyes of a Wraith.

The other hand was thrust towards Sheppards chest, and the Wraith began to feed.

Sheppard woke up in a cold sweat, gasping to catch every breath, Sheppard got out of bed, and went over to the mirror.

Turning on the light Sheppard saw something disturbing in the mirror, his hair was beginning to turn white, and there were wrinkles in his face.

Sheppard made a bee-line for the infirmary. But when he got there he spotted Rodney, Dr. Weir and Carson were talking.

"I think someone's trying to help him." Rodney said, in his 'we're screwed' tone.

"Who?" Weir demanded, it was Elizabeth Weir, but her tone indicated otherwise, it seemed so unfamiliar.

"He keeps seeing Wraith, maybe there's a clue." Rodney said.

"It's a possibility." Carson confirmed. His accent seemed off.

"Colonel Sheppard." Major Lorne came up from behind.

"Major Lorne?"

"What are you doing here?" Lorne inquired.

"Just came to have a talk with Beckett." Sheppard replied.

"Why don't we go talk to him together." Lorne said.

"Good idea." Sheppard agreed, trying to keep a friendly face on a situation that was obviously deteriorating.

A man that looked like Major Lorne escorted Colonel Sheppard into the infirmary to speak with people that looked and sounded like Weir, McKay, and Beckett.

Weir saw Major Lorne and Colonel Sheppard.

"What's this all about Major?"

"I found him eavesdropping outside." Major Lorne replied.

"I wasn't dropping any eaves!" Sheppard defended.

"So you heard." Weir said.

"What's going on?" Sheppard demanded.

Weir, Beckett, McKay, and Lorne looked at each other, then Beckett broke the silence.

"We didn't want to alarm you. But you may have been infected by a Wraith agent. The symptoms being, insomnia, paranoia, border-line psychosis."

"You haven't been your self, John." Weir said, something seemed out of place.

"When did I pick this up?" Sheppard asked.

"On your mission to M4X-639." Beckett added.

"How come Ronon, Teyla, and Rodney weren't infected?" Sheppard asked. It seemed the perfect defense. It was too perfect, nobody had an immediate response.

"That's what I thought." Sheppard said. "Major Lorne, sorry about this." Sheppard said before cold-clocking Lorne and taking his P-90, side arm and radio. Then exiting the infirmary.

Sheppard now knew there was almost nobody in the city he could trust, and in a matter of minutes there would be a large number of marines looking for him.

The only person he felt he could trust was a Wraith.

Well now that they know that Sheppard is suspicious of every one on the base except for Todd, who doesn't appear to be there. What is going to happen to Sheppard


	5. CH 5: Truth Revealed!

I would like to take the opportunity to point out that Sacred White Phoenix accidentally reveiwed my story under my name, no worries as he is family. I was just saying.

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Stargate Atlantis: Frame of Mind

**Ch 5 - Truth Revealed!**

It had been two hours since Sheppard fled from the infirmary and hid in one of the formerly flooded sections of the city, where the internal sensors were blinded.

It was odd that no one tried to contact him over the radio.

Even more strange was the city seemed more and more like a Wraith Hive ship.

"John Sheppard?" it was the familiar voice of Todd. Sheppard was a little apprehensive and suspicious, and yet he alerted the Wraith to his position.

"Why are you here?" Sheppard demanded.

"I am here to talk." Todd assured.

"Well then, talk!" Sheppard wearily snapped.

"What is the last thing you remember before . . ." Todd paused, unsure how to sum up the insanity that had ensued over the last six hours, Sheppard finished Todd's sentence.

"Before everyone in the city went off the deep end?"

Todd replied by a slight tilt of his head.

"I remember returning from a mission to M4X-639." Sheppard replied.

"Was there anything unusual about this . . . mission?" Todd inquired.

"I don't know if I should be talking with you about this." Sheppard resisted, but the Wraith persisted.

"There may be answers that you aren't aware of, I can help you find them. But first you need to answer my questions." Todd pushed, and Sheppard eventually divulged a summary of the mission.

"It was the sight of a Wraith outpost, but it had been attacked from orbit . . but nobody in this galaxy has the fire power to do the kind of damage that I saw. Except for the Replicators, but they've been sitting on their nanites hands for the last ten-thousand years."

"It might have been a Wraith hive ship that attacked." Sheppard decided. "The destruction of the outpost might have triggered enough secondary explosions."

Sheppard decided he would have to be happy with that answer, whether or not it made any sense.

"But that still doesn't explain what's going on here." Sheppard retorted.

"Maybe you're just being paranoid." Todd suggested.

"Is it paranoia if the world really is out get you?" Sheppard asked.

"Perhaps not." Todd replied. "But maybe you think the world doesn't make sense, and in order for you to make sense of it, you have to be sure that it makes no sense." Todd suggested.

Sheppard thought for a split second.

"I've got an idea." Sheppard said.

Sheppard knew the quickest way to where he was going, he knew what he would have to do, and he had the two authorization codes to make it happen, and make sure it could not be undone in time.

His plan: Activate the city's self-destruct.

As soon as he arrived. He began punching in the order to activate the self destuct and lock out everybody once it was activated. But before he could execute his plan he heard a voice trying to talk him down.

"Stand down, Colonel!" Dr. Weir demanded.

"It's funny, every time I get close to understanding what's going on here. There's someone to slow me down. Now why would that be?" Sheppard asked.

"I don't know what you're talking about." Weir defended.

"Sorry, something's wrong, and I have to find out what." Sheppard explained.

"By destroying the city, and killing everyone?" Weir challenged.

"I assume a team of Marines in on the way." Sheppard assumed.

"Two teams." Weir confirmed.

"Well, then. I'll just have to finish before they get here." Sheppard said as he finished typing the last of the codes in.

"Tell me what's going on, or I blow the city." Sheppard threatened, then everything became clear.

"You're not Elizabeth . . . you're a Replicator!"

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The depressing thing is Sacred White Phoenix got it spot on! Way to go S.W.P. any way I'm glad you enjoyed this so much. I'll have to come up with something else later on. But the story is not over yet.


	6. CH 6: The Final Confrontation

Thank you so much for your reviews and input, please don't forget, I don't bite when I recieve a review. My head just gets bigger. lol.

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Stargate Atlantis - Frame of Mind -

CH 6 - The Final Confrontation.

The Elizabeth Replicator smiled, a crooked smile.

"When did you know?"

"About the time I fed on McKay." Sheppard declared.

The Weir Replicator circled Sheppard looking for a more defensible position.

Sheppard saw the threat and pressed the enter key, initiating a thirty second countdown until the self-destruct went off.

"If this city is destroyed, then you will die, John." the Weir Replicator threatened.

"Works for me." Sheppard casually replied as the self-destruct went off.

A Replicator pulled their hand from Sheppard's forehead.

"Your powers of resistence are . . . remarkable." Oberoth commended darkly.

"Thanks." Sheppard coughed out. Then caught a glimpse of others in the cell with him: Ronon, Teyla, and McKay.

Oberoth walked out, and four Replicator guards stood watch over the cell, making sure nobody escaped.

Sheppard's memories of the real world came back quickly.

"Are you alright?" Ronon asked.

"Yeah, I think so." Sheppard looked towards the guards.

"Did they capture Major Lorne?"

The 'whooshing' sound from an A.R.G. discharging could be heard, followed by millions of nanite cells hitting the ground.

"I guess that's a 'no'." Sheppard said.

Major Lorne's team entered and wiped out the four Replicator guards.

"Sorry I'm late kids." Lorne said.

"That's alright, just get us out of here." Rodney pleaded.

Lorne disengaged the door lock. The force fields dropped and the door opened.

"We've got to get to the jumper bay." Sheppard decreed.

"Not a problem, I had my team set up some 'distractions' in some crucial areas." Lorne informed, then armed Sheppard and Ronon each with an A.R.G. Then Sheppard lead the way out of the brig.

Moving swiftly through the corridors they met with no resistance.

"I've got a bad feeling about this." Ronon declared.

"You're not the only one, Chewie." Sheppard replied.

"We don't have to worry much longer, the jumper bay is just down the corridor." Major Lorne said, hoping it would be comforting.

"That's the problem, we haven't seen any Replicators, they're probably got some guards posted in the jumper bay." Sheppard suspected.

Shepard and Lorne's teams ran the last few dozen meters to the jumper bay. Much to everyone's surprise there were no guards, until they arrived at the first open jumper.

"I figured you'd try something foolish." Oberoth declared.

Then a few dozen Replicator guards filed into place behind Sheppard and Lorne's teams.

Sheppard looked at Lorne.

"What was it you were saying about some 'distractions'?" Sheppard asked.

At those words an Anti-Replicator field swept through the jumper bay, and all the Replicators fell apart.

"I guess that answers that." Sheppard said, then closed the jumper's rear door, took a seat in the pilots seat and dialed the Stargate, opened the lower door, lowered the jumper into the Replicator gate room, and zipped through the active Stargate.

Six hours later, in the lost city of the Ancients, Sheppard over looked the massive city.

Sheppard was lost in thought when Weir found him.

"Am I interrupting, John?" Weir asked, announcing her presence.

Sheppard noticed his commander, and gave her his full attention.

"Not at all." Sheppard replied.

"I just finished reading the report, they must have put you through the ringer." Weir surmised.

"Yeah. They did. The worst part is not knowing if I was in the real world, or if I was going to wake up in my quarters again." Sheppard explained.

"Are you sure you're . . ." Weir couldn't find the right word.

"Not in a Replicator induced nightmare? Not really." Sheppard finished. "But at least I haven't seen any Wraith for the last six hours."

"But?" Weir prodded.

"It seemed too easy." Sheppard said, then gazed out toward the horizon while Weir walked away, Sheppard's comment stopped her.

"That doesn't mean I'm letting my guard down."

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Thanks again for reading and reviewing. I appreciate all of your comments. My next work is in progress, and it's a doozy.


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